def test_query_with_fields_as_list(self):
qres1 = self.mg.query("entrezgene:1017", fields="name,symbol,refseq")
qres2 = self.mg.query("entrezgene:1017",
fields=["name", "symbol", "refseq"])
self.assertTrue('hits' in qres1)
self.assertEqual(len(qres1['hits']), 1)
self.assertEqual(descore(qres1['hits']), descore(qres2['hits']))
def test_querymany_fields(self):
qres1 = self.mg.findgenes([1017, 'CDK2'], scopes='entrezgene,symbol', fields=['uniprot', 'unigene'], species=9606, verbose=False)
self.assertEqual(len(qres1), 2)
qres2 = self.mg.findgenes([1017, 'CDK2'], scopes='entrezgene,symbol', fields='uniprot,unigene', species=9606, verbose=False)
self.assertEqual(len(qres2), 2)
self.assertEqual(descore(qres1), descore(qres2))
def test_querymany_step(self):
qres1 = self.mv.querymany(self.query_list2, scopes='dbsnp.rsid', verbose=False)
default_step = self.mv.step
self.mv.step = 3
qres2 = self.mv.querymany(self.query_list2, scopes='dbsnp.rsid', verbose=False)
self.mv.step = default_step
# self.assertEqual(qres1, qres2, (qres1, qres2))
self.assertEqual(descore(qres1), descore(qres2))
def test_querymany_step(self):
qres1 = self.mg.querymany(self.query_list1, scopes='reporter')
default_step = self.mg.step
self.mg.step = 3
qres2 = self.mg.querymany(self.query_list1, scopes='reporter')
self.mg.step = default_step
qres1 = descore(sorted(qres1, key=lambda doc: doc['_id']))
qres2 = descore(sorted(qres2, key=lambda doc: doc['_id']))
self.assertEqual(qres1, qres2)
def test_querymany_fields(self):
ids = ['COSM1362966', 'COSM990046', 'COSM1392449']
qres1 = self.mv.querymany(ids, scopes='cosmic.cosmic_id', fields=['cosmic.tumor_site', 'cosmic.cosmic_id'], verbose=False)
self.assertEqual(len(qres1), 3)
qres2 = self.mv.querymany(ids, scopes='cosmic.cosmic_id', fields='cosmic.tumor_site,cosmic.cosmic_id', verbose=False)
self.assertEqual(len(qres2), 3)
self.assertEqual(descore(qres1), descore(qres2))
def test_querymany_step(self):
qres1 = self.mc.querymany(self.query_list1,
scopes='_id',
fields="pubchem")
default_step = self.mc.step
self.mc.step = 3
qres2 = self.mc.querymany(self.query_list1,
scopes='_id',
fields="pubchem")
self.mc.step = default_step
qres1 = descore(sorted(qres1, key=lambda doc: doc['_id']))
qres2 = descore(sorted(qres2, key=lambda doc: doc['_id']))
self.assertEqual(qres1, qres2)
def test_querymany_fields(self):
qres1 = self.mc.querymany(
["DB00536", 'DB00533'],
scopes='drugbank.id',
fields=['drugbank.name', 'unii.registry_number'],
verbose=False)
self.assertEqual(len(qres1), 2)
qres2 = self.mc.querymany(["DB00536", 'DB00533'],
scopes='drugbank.id',
fields='drugbank.name,unii.registry_number',
verbose=False)
self.assertEqual(len(qres2), 2)
self.assertEqual(descore(qres1), descore(qres2))
def test_querymany_fields(self):
qres1 = self.mc.querymany(
['CHEBI:31690', 'CHEBI:15365'],
scopes='chebi.id',
fields=['chebi.name', 'unii.registry_number'],
verbose=False)
self.assertEqual(len(qres1), 2)
qres2 = self.mc.querymany(['CHEBI:31690', 'CHEBI:15365'],
scopes='chebi.id',
fields='chebi.name,unii.registry_number',
verbose=False)
self.assertEqual(len(qres2), 2)
self.assertEqual(descore(qres1), descore(qres2))